7EKA | pdb_00007eka

crystal structure of epigallocatechin binding with alpha-lactalbumin

  • Classification: LIGASE
  • Organism(s): Bos taurus
  • Expression System: Bos taurus
  • Mutation(s): No 

  • Deposited: 2021-04-05 Released: 2023-11-08 
  • Deposition Author(s): Ma, J., Yao, Q., Chen, X., Zang, J.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 
    0.176 (Depositor), 0.184 (DCC) 
  • R-Value Work: 
    0.168 (Depositor) 
  • R-Value Observed: 
    0.169 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7EKA

This is version 1.2 of the entry. See complete history

Literature

Weak Binding of Epigallocatechin to alpha-Lactalbumin Greatly Improves Its Stability and Uptake by Caco-2 Cells.

Ma, J.Yao, Q.Chen, X.Lv, C.Zang, J.Zhao, G.

(2021) J Agric Food Chem 69: 8482-8491

  • DOI: https://doi.org/10.1021/acs.jafc.1c03427
  • Primary Citation Related Structures: 
    7EKA

  • PubMed Abstract: 

    Improving the stability and bioavailability of catechins is of great importance. Epigallocatechin (EGC), the major catechin in green tea, is a potent antioxidant with numerous attributed health benefits. However, the low permeability and stability limit its enrichment in the diet for preventive medicine. In this study, we explored the interaction of EGC and α-lactalbumin by spectroscopic, thermodynamic, and crystallographic methods. The isothermal titration calorimetry experiments elucidated that α-lactalbumin binds to EGC at a ratio of 1:1 with a low affinity of (4.01 ± 0.11) × 10 5 M -1 . A crystal structure solved at a high resolution (1.2 Å) provided direct evidence for the weak interaction between EGC and α-lactalbumin at an atomic level. The novel binding site was discovered at the exterior surface of α-lactalbumin for the first time, supporting a new binding behavior. Consequently, our results demonstrated that the binding of α-lactalbumin to EGC could protect EGC against light-induced, thermal-induced, and pH-induced damage. More importantly, the formed complex has better bioaccessibility than unbound EGC, which was approved by a cell absorption experiment. Such research is beneficial for designing protein-based nanocarriers for polyphenols.


  • Organizational Affiliation
    • College of Food Science and Nutritional Engineering, China Agricultural University, Beijing Key Laboratory of Functional Food from Plant Resources, Beijing 100083, China.

Macromolecule Content 

  • Total Structure Weight: 14.27 kDa 
  • Atom Count: 1,179 
  • Modeled Residue Count: 121 
  • Deposited Residue Count: 121 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Alpha-lactalbumin121Bos taurusMutation(s): 0 
Gene Names: LALBAALACTA
UniProt
Find proteins for P00711 (Bos taurus)
Explore P00711 
Go to UniProtKB:  P00711
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00711
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EGT

Query on EGT



Download:Ideal Coordinates CCD File
B [auth A]2-(3,4,5-TRIHYDROXY-PHENYL)-CHROMAN-3,5,7-TRIOL
C15 H14 O7
XMOCLSLCDHWDHP-IUODEOHRSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free:  0.176 (Depositor), 0.184 (DCC) 
  • R-Value Work:  0.168 (Depositor) 
  • R-Value Observed: 0.169 (Depositor) 
Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.344α = 90
b = 69.344β = 90
c = 59.553γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data collection
HKL-3000data scaling
PHENIXmodel building
PHENIXphasing
HKL-3000data reduction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31730069

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-08
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Structure summary
  • Version 1.2: 2026-03-04
    Changes: Refinement description